My two cents theory is that Endacopia is a game about growing up on an abusive family, and how you deal with it when you grow up.
Timesville, Misery Town and the Factory seem like a child's make-believe coping of how to deal with topics that I've heard or dealt with while growing up. Specifically, the Factory is the concretization of the idea that being an adult means being super boring and living for the job, while minimizing or downright eliminating anything that makes you be you and not just yet another cog in the machine. Misery Town is the demonization of self-expression and seeking your own dreams and doing what your heart desires despite not leading you to prosperity. And Timesville is the fearmongering ideas taught by your parents of how the world is full of evil adults and problematic people and crappy, nosy neighbors who perhaps pry too much and care too much about the child of an abusive home.
Yes there is also a really clear criticism in the Factory of late-stage capitalism and how corporate grind is a meaningless rat race that places you in arbitrary positions depending on a worth scale that is nonsensical and counterintuitive to even your own self-preservation; and of celebrity culture and showbiz and Hollywood-style fame in Misery Town's whole clown hierarchy system. But also I feel like it is all also very heavily filtered through the eyes of a child, as if the child was playing make-believe of said concepts to deal with whatever their parents tell them they should do or be like, how the world works, or what expect from adult life.
But I don't think it is just a make-believe and that's it, as a matter of fact, given that Mellow meets and helps out and gets helped out by so many others he meets in these different areas, and in ending B you get to live a life outside of said chaotic, abusive household with said people, it feels like it's the idea of confronting all those pre-conceived notions of the world that you learned through the lens of a child in an abusive environment, and figuring it out that things are not all that bad, and you can actually find people who will love and care for you beyond your family. Basically, ending B is the idea of "blood of the covenant is thicker than water of the womb."
Meanwhile, ending A is the other way you escape said situation, but you don't escape the way it damaged you, finding yourself still trapped in one way or another in abusive situations. You give means to a destructive parasite to escape the dying world which allows you to escape your situation, but that parasite will never be your friend, they were doing things just for their own sake, and hope to never see you again, and even when you try to find comfort with them they tell you that things are done and they are to go on their own way. Be it that an analog to an abusive partner or friend you get together with to escape your own abusive home, or your own worst traits that you leveraged to escape home, you are never free from the trauma cycle in this path, and you threw away everyone who ever cared for you.
Ending C is perhaps the most cryptic for me, also because it is the most lore-heavy, leaving little room for interpretation, but given that it doesn't seem like it is a good ending, given that everything, including yourself, gets swallowed up by the revived body of god, I would assume it is straight up the worst path you can end up taking in regards to growing up in an abusive environment. It is the path where you never leave, and get consumed by it, be it psychologically or perhaps even physically. You get so tangled up trying to help a dying cause, trying to play the martyr for your family, doing everything to try to save their relationship despite not being something you have power over nor should be responsible for, that you end up either broken down mentally by such a state of helplessness and cruelty imposed by others, or you end up, well, lifeless, by others or your own hands.
Anyways, this is what I theorize, about those things, there are so many more concepts that are so interesting in there, the Surgeon for example is a treasure trove of psychological analysis, but yeah this is my overall theory about the message of the game.
